Soy Endophytes CO2 Full Code
Connor Morozumi
most recent edits 17 June 2025
1 Load pkgs
library(tidyverse)## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.3 ✔ readr 2.1.4
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## ✔ ggplot2 3.4.4 ✔ tibble 3.2.1
## ✔ lubridate 1.9.3 ✔ tidyr 1.3.0
## ✔ purrr 1.0.2
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## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(here)## here() starts at /Users/connor/Dropbox/SoyEndophytes/public_repolibrary(patchwork)
library(cowplot)##
## Attaching package: 'cowplot'
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## The following object is masked from 'package:patchwork':
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## align_plots
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## stamplibrary(ggVennDiagram)##
## Attaching package: 'ggVennDiagram'
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## unitelibrary(ggpubr)##
## Attaching package: 'ggpubr'
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## get_legendlibrary(vegan)## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.6-4library(phyloseq)## Warning: package 'phyloseq' was built under R version 4.2.2library(SpiecEasi)
library(NetCoMi)## 2 Read in data
cleaned.files= here::here("datasets")
net.loc= here("network_analysis")
output.loc= here("outputs")
#its1
its1=read.csv(file= paste0(cleaned.files,"/cleaned.ASVs.ITS1.csv"), row.names = "X")
its1.net= read_csv(file= paste0(cleaned.files,"/cleaned.ASVs.ITS1.csv"))## New names:
## Rows: 117 Columns: 423
## ── Column specification
## ──────────────────────────────────────────────────────── Delimiter: "," chr
## (1): ...1 dbl (422): Epicoccum dendrobii, Epicoccum dendrobii.1, Epicoccum
## thailandicu...
## ℹ Use `spec()` to retrieve the full column specification for this data. ℹ
## Specify the column types or set `show_col_types = FALSE` to quiet this message.
## • `` -> `...1`#its2
its2 = read.csv(file= paste0(cleaned.files, "/cleaned.ASVs.its2.csv"), row.names = "X")
its2.net = read_csv(file= paste0(cleaned.files, "/cleaned.ASVs.its2.csv"))## New names:
## Rows: 117 Columns: 1062
## ── Column specification
## ──────────────────────────────────────────────────────── Delimiter: "," chr
## (1): ...1 dbl (1061): Epicoccum sp., Cladosporium ramotenellum, Didymella sp.,
## Paracon...
## ℹ Use `spec()` to retrieve the full column specification for this data. ℹ
## Specify the column types or set `show_col_types = FALSE` to quiet this message.
## • `` -> `...1`#bacteria
bac= read.csv(file= paste0(cleaned.files,"/cleaned.ASVs.bacteria.csv"), row.names = "X")
bac.net= read_csv(file= paste0(cleaned.files,"/cleaned.ASVs.bacteria.csv"))## New names:
## Rows: 117 Columns: 214
## ── Column specification
## ──────────────────────────────────────────────────────── Delimiter: "," chr
## (1): ...1 dbl (213): Methylobacterium-Methylorubrum sp.,
## Methylobacterium-Methylorubru...
## ℹ Use `spec()` to retrieve the full column specification for this data. ℹ
## Specify the column types or set `show_col_types = FALSE` to quiet this message.
## • `` -> `...1`# two additional ones for higher level taxa summaries
# bac.asvnos= read.csv(file= paste0(cleaned.files,"/cleaned.nothost.bacteria.asv_labeled_by_asv_no.csv"), row.names = "X")
#
# tax dfs
bac.tax= read.csv(file= paste0(cleaned.files,"/cleaned.nothost.bacteria.taxa.matched_to_asv_no.csv"), row.names = "X")
its1.tax= read.csv(file= paste0(cleaned.files,"/cleaned.nothost.its1.taxa.matched_to_asv_no.csv"), row.names = "X")
its2.tax= read.csv(file= paste0(cleaned.files,"/cleaned.nothost.its2.taxa.matched_to_asv_no.csv"), row.names = "X")
#metadata
meta= read.csv(file= paste0(cleaned.files, "/cleaned.meta.csv"), sep=",", header = T)2.1 Cleaning
# change plot names for congruence with metadata and taxa dfs
meta$site= sub("_", "-", meta$site)
its1= its1 %>%
rownames_to_column("site")
its1$site= sub("_", "-", its1$site)
its1 = its1 %>%
column_to_rownames("site")
meta.lite= meta %>%
dplyr::select(site, CO2, plot, rep)
# Clean up family names for more readable legend
its1.tax$Family.legend= gsub(".*__","",its1.tax$Family)
its2.tax$Family.legend= gsub(".*__","",its2.tax$Family)
# sample ID
# fix sample names
names(its1.net)[1] ="Sample"
its1.net$Sample= sub("_", "-", its1.net$Sample)
names(its2.net)[1] ="Sample"
names(bac.net)[1] ="Sample"3 SUMMARY STATS
3.1 Read counts
# link meta to asv dfs too
## its1
read.counts.its1= its1 %>%
rownames_to_column("site") %>%
full_join(., meta.lite) %>%
dplyr::select(-c(plot, rep)) %>%
group_split(CO2)## Joining with `by = join_by(site)`names(read.counts.its1)<- c("control", "elevated")
read.counts.its1= map(read.counts.its1, dplyr::select,!CO2)
read.counts.its1= map(read.counts.its1, column_to_rownames, "site")
# filter out columns that are completely blank, these can be induced once the dataset is split by treatment
no.zeros.its1=list()
no.zeros.its1$control=read.counts.its1$control[colSums(read.counts.its1$control, na.rm = TRUE) > 0]
no.zeros.its1$elevated=read.counts.its1$elevated[colSums(read.counts.its1$elevated, na.rm = TRUE) > 0]
## bac
read.counts.bac= bac %>%
rownames_to_column("site") %>%
full_join(., meta.lite) %>%
dplyr::select(-c( plot, rep)) %>%
group_split(CO2)## Joining with `by = join_by(site)`names(read.counts.bac)<- c("control", "elevated")
read.counts.bac= map(read.counts.bac, dplyr::select,!CO2)
read.counts.bac= map(read.counts.bac, column_to_rownames, "site")
no.zeros.bac=list()
no.zeros.bac$control=read.counts.bac$control[colSums(read.counts.bac$control, na.rm = TRUE) > 0]
no.zeros.bac$elevated=read.counts.bac$elevated[colSums(read.counts.bac$elevated, na.rm = TRUE) > 0]
## its2
read.counts.its2= its2 %>%
rownames_to_column("site") %>%
full_join(., meta.lite) %>%
dplyr::select(-c(plot, rep)) %>%
group_split(CO2)## Joining with `by = join_by(site)`names(read.counts.its2)<- c("control", "elevated")
read.counts.its2= map(read.counts.its2, dplyr::select,!CO2)
read.counts.its2= map(read.counts.its2, column_to_rownames, "site")
map(read.counts.its2, sum)## $control
## [1] 752887
##
## $elevated
## [1] 964266no.zeros.its2=list()
no.zeros.its2$control=read.counts.its2$control[colSums(read.counts.its2$control, na.rm = TRUE) > 0]
no.zeros.its2$elevated=read.counts.its2$elevated[colSums(read.counts.its2$elevated, na.rm = TRUE) > 0]## sum read counts across primers
its1.read.sums= map(no.zeros.its1, sum)
its2.read.sums= map(no.zeros.its2, sum)
bac.read.sums= map(no.zeros.bac, sum)
its1.read.sums.tot= sum(unlist(its1.read.sums, recursive=FALSE))
its2.read.sums.tot= sum(unlist(its2.read.sums, recursive=FALSE))
bac.read.sums.tot= sum(unlist(bac.read.sums, recursive=FALSE))4 COMMUNITY METRICS
4.1 Richness and diversity
Per sample
#richness per sample
bac$richness= rowSums(bac > 0)
its1$richness= rowSums(its1 > 0)
its2$richness= rowSums(its2 > 0)
# shannon, simp
bac$H = diversity(bac)
its1$H = diversity(its1)
its2$H = diversity(its2)
bac$simp = diversity(bac, "simpson")
its1$simp = diversity(its1, "simpson")
its2$simp = diversity(its2, "simpson")Per plot To calculate per plot richness we are going to have to do some extra massaging
plot.rich.bac= bac %>%
rownames_to_column("site")
plot.rich.its1= its1 %>%
rownames_to_column("site")
plot.rich.its2= its2 %>%
rownames_to_column("site")
plot.rich.bac=full_join(plot.rich.bac, meta.lite)## Joining with `by = join_by(site)`plot.rich.its1=full_join(plot.rich.its1, meta.lite)## Joining with `by = join_by(site)`plot.rich.its2=full_join(plot.rich.its2, meta.lite)## Joining with `by = join_by(site)`Link to metadata
# rownames to cols to link meta data in
bac.div= bac %>%
dplyr::select(richness, H, simp) %>%
rownames_to_column("site")
its1.div= its1 %>%
dplyr::select(richness, H, simp) %>%
rownames_to_column("site")
its2.div= its2 %>%
dplyr::select(richness, H, simp) %>%
rownames_to_column("site")
# link to meta
bac.div= full_join(bac.div, meta.lite)## Joining with `by = join_by(site)`its1.div= full_join(its1.div, meta.lite)## Joining with `by = join_by(site)`its2.div= full_join(its2.div, meta.lite)## Joining with `by = join_by(site)`4.2 Composition
Transform data to proportions or apply Hellinger
ITS1.asv.prop=prop.table(as.matrix(its1),1)
ITS1.asv.hell <- decostand(its1, "hellinger")
its2.asv.prop=prop.table(as.matrix(its2),1)
its2.asv.hell <- decostand(its2, "hellinger")
bacteria.asv.prop=prop.table(as.matrix(bac),1)
bacteria.asv.hell <- decostand(bac, "hellinger")Visualization
NMDS for each primer on the transformed mat
ITS1
its1.mds <- metaMDS(ITS1.asv.prop)## Run 0 stress 0.2066101
## Run 1 stress 0.2313255
## Run 2 stress 0.2180168
## Run 3 stress 0.2017663
## ... New best solution
## ... Procrustes: rmse 0.06273509 max resid 0.3785614
## Run 4 stress 0.2107423
## Run 5 stress 0.2005392
## ... New best solution
## ... Procrustes: rmse 0.03079813 max resid 0.2249917
## Run 6 stress 0.1999325
## ... New best solution
## ... Procrustes: rmse 0.04999547 max resid 0.4502096
## Run 7 stress 0.2022238
## Run 8 stress 0.2150842
## Run 9 stress 0.1997167
## ... New best solution
## ... Procrustes: rmse 0.04094578 max resid 0.4052451
## Run 10 stress 0.2043617
## Run 11 stress 0.2065799
## Run 12 stress 0.2040572
## Run 13 stress 0.2157917
## Run 14 stress 0.1987304
## ... New best solution
## ... Procrustes: rmse 0.04639118 max resid 0.2758157
## Run 15 stress 0.2412488
## Run 16 stress 0.2033998
## Run 17 stress 0.199623
## Run 18 stress 0.2319903
## Run 19 stress 0.2245278
## Run 20 stress 0.23903
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 1: no. of iterations >= maxit
## 19: stress ratio > sratmaxits1.mds.mds.3 <- metaMDS(ITS1.asv.prop, k=3)## Run 0 stress 0.1202522
## Run 1 stress 0.1253933
## Run 2 stress 0.1203019
## ... Procrustes: rmse 0.005123648 max resid 0.04864147
## Run 3 stress 0.1202526
## ... Procrustes: rmse 0.0008150113 max resid 0.005710849
## ... Similar to previous best
## Run 4 stress 0.1214577
## Run 5 stress 0.1221056
## Run 6 stress 0.1218708
## Run 7 stress 0.1218712
## Run 8 stress 0.1311642
## Run 9 stress 0.1457618
## Run 10 stress 0.1218723
## Run 11 stress 0.1203025
## ... Procrustes: rmse 0.005121691 max resid 0.04865503
## Run 12 stress 0.1202528
## ... Procrustes: rmse 0.0008590684 max resid 0.007162997
## ... Similar to previous best
## Run 13 stress 0.1253963
## Run 14 stress 0.122063
## Run 15 stress 0.1221432
## Run 16 stress 0.1221904
## Run 17 stress 0.125394
## Run 18 stress 0.120267
## ... Procrustes: rmse 0.001957128 max resid 0.01780351
## Run 19 stress 0.1203302
## ... Procrustes: rmse 0.005250133 max resid 0.04853555
## Run 20 stress 0.1504365
## *** Best solution repeated 2 timesmetaMDS(ITS1.asv.prop, k=3, previous.best = its1.mds.mds.3)## Starting from 3-dimensional configuration
## Run 0 stress 0.1202522
## Run 1 stress 0.1221793
## Run 2 stress 0.1543107
## Run 3 stress 0.1296756
## Run 4 stress 0.1219415
## Run 5 stress 0.1219415
## Run 6 stress 0.1202594
## ... Procrustes: rmse 0.00132137 max resid 0.0117324
## Run 7 stress 0.1221693
## Run 8 stress 0.1221717
## Run 9 stress 0.1223207
## Run 10 stress 0.1203027
## ... Procrustes: rmse 0.005120812 max resid 0.04876093
## Run 11 stress 0.127147
## Run 12 stress 0.1202522
## ... Procrustes: rmse 0.0003115428 max resid 0.002256778
## ... Similar to previous best
## Run 13 stress 0.1308975
## Run 14 stress 0.1219415
## Run 15 stress 0.1219417
## Run 16 stress 0.1270295
## Run 17 stress 0.1282541
## Run 18 stress 0.1274195
## Run 19 stress 0.1202519
## ... New best solution
## ... Procrustes: rmse 0.0006577628 max resid 0.004218151
## ... Similar to previous best
## Run 20 stress 0.1288932
## *** Best solution repeated 1 times##
## Call:
## metaMDS(comm = ITS1.asv.prop, k = 3, previous.best = its1.mds.mds.3)
##
## global Multidimensional Scaling using monoMDS
##
## Data: ITS1.asv.prop
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1202519
## Stress type 1, weak ties
## Best solution was repeated 1 time in 40 tries
## The best solution was from try 39 (random start)
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'ITS1.asv.prop'#hellinger
its1.mds.hell <- metaMDS(ITS1.asv.hell)## Run 0 stress 0.2302418
## Run 1 stress 0.2438084
## Run 2 stress 0.2323092
## Run 3 stress 0.2300196
## ... New best solution
## ... Procrustes: rmse 0.00619494 max resid 0.06448405
## Run 4 stress 0.2353881
## Run 5 stress 0.2319402
## Run 6 stress 0.2314957
## Run 7 stress 0.25581
## Run 8 stress 0.2309687
## Run 9 stress 0.2301698
## ... Procrustes: rmse 0.003744664 max resid 0.02944566
## Run 10 stress 0.2376224
## Run 11 stress 0.2455472
## Run 12 stress 0.2317653
## Run 13 stress 0.2382812
## Run 14 stress 0.2307375
## Run 15 stress 0.2300196
## ... New best solution
## ... Procrustes: rmse 0.0005442131 max resid 0.00422123
## ... Similar to previous best
## Run 16 stress 0.2315796
## Run 17 stress 0.230111
## ... Procrustes: rmse 0.002907652 max resid 0.0253345
## Run 18 stress 0.2308776
## Run 19 stress 0.4134527
## Run 20 stress 0.2379424
## *** Best solution repeated 1 timesits1.mds.3.hell <- metaMDS(ITS1.asv.hell, k=3)## Run 0 stress 0.1632476
## Run 1 stress 0.1632741
## ... Procrustes: rmse 0.0268868 max resid 0.268996
## Run 2 stress 0.1632468
## ... New best solution
## ... Procrustes: rmse 0.000177154 max resid 0.001699588
## ... Similar to previous best
## Run 3 stress 0.1632461
## ... New best solution
## ... Procrustes: rmse 0.0001052523 max resid 0.0007078326
## ... Similar to previous best
## Run 4 stress 0.1632543
## ... Procrustes: rmse 0.004041176 max resid 0.03915495
## Run 5 stress 0.1640441
## Run 6 stress 0.1632474
## ... Procrustes: rmse 0.003151712 max resid 0.03056742
## Run 7 stress 0.1662856
## Run 8 stress 0.1632748
## ... Procrustes: rmse 0.02738609 max resid 0.274164
## Run 9 stress 0.1639667
## Run 10 stress 0.166668
## Run 11 stress 0.1632662
## ... Procrustes: rmse 0.00500943 max resid 0.04860608
## Run 12 stress 0.1632597
## ... Procrustes: rmse 0.004487319 max resid 0.04326371
## Run 13 stress 0.1632487
## ... Procrustes: rmse 0.0007699863 max resid 0.004556935
## ... Similar to previous best
## Run 14 stress 0.1632756
## ... Procrustes: rmse 0.005761526 max resid 0.05594761
## Run 15 stress 0.1647938
## Run 16 stress 0.1647923
## Run 17 stress 0.1632744
## ... Procrustes: rmse 0.02725636 max resid 0.2729225
## Run 18 stress 0.1641238
## Run 19 stress 0.1648895
## Run 20 stress 0.1659173
## *** Best solution repeated 2 timesmetaMDS(ITS1.asv.hell, k=3, previous.best = its1.mds.3.hell)## Starting from 3-dimensional configuration
## Run 0 stress 0.1632461
## Run 1 stress 0.164793
## Run 2 stress 0.1632471
## ... Procrustes: rmse 0.0001806698 max resid 0.001622254
## ... Similar to previous best
## Run 3 stress 0.1648136
## Run 4 stress 0.164887
## Run 5 stress 0.1633711
## ... Procrustes: rmse 0.01036408 max resid 0.1009508
## Run 6 stress 0.1633175
## ... Procrustes: rmse 0.008097086 max resid 0.07872191
## Run 7 stress 0.163263
## ... Procrustes: rmse 0.004731158 max resid 0.04557621
## Run 8 stress 0.1634559
## ... Procrustes: rmse 0.007804179 max resid 0.06323481
## Run 9 stress 0.1632745
## ... Procrustes: rmse 0.02700637 max resid 0.2702803
## Run 10 stress 0.1632426
## ... New best solution
## ... Procrustes: rmse 0.001449912 max resid 0.01408879
## Run 11 stress 0.1632488
## ... Procrustes: rmse 0.001910242 max resid 0.01837757
## Run 12 stress 0.163248
## ... Procrustes: rmse 0.001631157 max resid 0.01580063
## Run 13 stress 0.1653427
## Run 14 stress 0.1632739
## ... Procrustes: rmse 0.02834993 max resid 0.2845359
## Run 15 stress 0.1632468
## ... Procrustes: rmse 0.001582545 max resid 0.01518116
## Run 16 stress 0.1632749
## ... Procrustes: rmse 0.0285043 max resid 0.2860614
## Run 17 stress 0.1652667
## Run 18 stress 0.1645012
## Run 19 stress 0.1632556
## ... Procrustes: rmse 0.002736291 max resid 0.02640758
## Run 20 stress 0.1632751
## ... Procrustes: rmse 0.0284876 max resid 0.2858805
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 10: no. of iterations >= maxit
## 10: stress ratio > sratmax##
## Call:
## metaMDS(comm = ITS1.asv.hell, k = 3, previous.best = its1.mds.3.hell)
##
## global Multidimensional Scaling using monoMDS
##
## Data: ITS1.asv.hell
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1632426
## Stress type 1, weak ties
## Best solution was not repeated after 40 tries
## The best solution was from try 30 (random start)
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'ITS1.asv.hell'A three dim k=3 solution is better
nmds.its1= its1.mds.mds.3 ## CHANGE ME
#site scores
data.scores.its1 <- as.data.frame(scores(nmds.its1)$sites) #Using the scores function from vegan to extract the site scores and convert to a data.frame
data.scores.its1$site <- rownames(data.scores.its1) # create a column of site names, from the rownames of data.scores
data.scores.its1=full_join(data.scores.its1, meta)## Joining with `by = join_by(site)`#species scores
species.scores.its1 <- as.data.frame(scores(nmds.its1, "species")) #Using the scores function from vegan to extract the species scores and convert to a data.frame
species.scores.its1$species <- rownames(species.scores.its1) # create a column of species, from the rownames of species.scoresits1.A= ggplot(data= data.scores.its1,aes(x=NMDS1,y=NMDS2,shape= CO2,colour=CO2)) +
#geom_text(data=species.scores.its1,aes(x=NMDS1,y=NMDS2,label=species),alpha=0.5) + # add the species labels
geom_point(size=3) + # add the point markers
#geom_text(data=data.scores.its1,aes(x=NMDS1,y=NMDS2,label=site),size=6,vjust=0) + # add the site labels
scale_colour_manual(values=c("Elevated" = "red", "Control" = "blue")) +
coord_equal() +
theme_bw()+
guides(color=guide_legend(expression(paste("CO"["2"]))), shape = FALSE)## Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
## of ggplot2 3.3.4.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.if("NMDS3" %in% colnames(data.scores.its1) ==TRUE){
its1.B=ggplot(data= data.scores.its1,aes(x=NMDS1,y=NMDS3,shape= CO2,colour=CO2)) +
#geom_text(data=species.scores.its1,aes(x=NMDS1,y=NMDS2,label=species),alpha=0.5) + # add the species labels
geom_point(size=3) + # add the point markers
#geom_text(data=data.scores.its1,aes(x=NMDS1,y=NMDS2,label=site),size=6,vjust=0) + # add the site labels
scale_colour_manual(values=c("Elevated" = "red", "Control" = "blue")) +
coord_equal() +
theme_bw()+
guides(color=guide_legend(expression(paste("CO"["2"]))), shape = FALSE)
}
#axis 2 vs 3
if("NMDS3" %in% colnames(data.scores.its1) ==TRUE){
its1.C=ggplot(data= data.scores.its1,aes(x=NMDS2,y=NMDS3,shape= CO2,colour=CO2)) +
#geom_text(data=species.scores.its1,aes(x=NMDS1,y=NMDS2,label=species),alpha=0.5) + # add the species labels
geom_point(size=3) + # add the point markers
#geom_text(data=data.scores.its1,aes(x=NMDS1,y=NMDS2,label=site),size=6,vjust=0) + # add the site labels
scale_colour_manual(values=c("Elevated" = "red", "Control" = "blue")) +
coord_equal() +
theme_bw()+
guides(color=guide_legend(expression(paste("CO"["2"]))), shape = FALSE)
}
its1.all= its1.A + its1.B + its1.Cits2
its2.mds.hell <- metaMDS(its2.asv.hell)## Run 0 stress 0.2371546
## Run 1 stress 0.2468062
## Run 2 stress 0.2434688
## Run 3 stress 0.2401786
## Run 4 stress 0.2472459
## Run 5 stress 0.254371
## Run 6 stress 0.2426449
## Run 7 stress 0.2402574
## Run 8 stress 0.2437059
## Run 9 stress 0.2434794
## Run 10 stress 0.244101
## Run 11 stress 0.2565453
## Run 12 stress 0.2464406
## Run 13 stress 0.2396452
## Run 14 stress 0.2519282
## Run 15 stress 0.2484724
## Run 16 stress 0.2416936
## Run 17 stress 0.2461888
## Run 18 stress 0.2468827
## Run 19 stress 0.2487219
## Run 20 stress 0.2502629
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 7: no. of iterations >= maxit
## 13: stress ratio > sratmaxits2.mds.hell.3 <- metaMDS(its2.asv.hell, k=3)## Run 0 stress 0.1795205
## Run 1 stress 0.1911154
## Run 2 stress 0.1833896
## Run 3 stress 0.1859847
## Run 4 stress 0.1808877
## Run 5 stress 0.1876924
## Run 6 stress 0.182177
## Run 7 stress 0.1911371
## Run 8 stress 0.1803418
## Run 9 stress 0.1811293
## Run 10 stress 0.1795707
## ... Procrustes: rmse 0.00636268 max resid 0.06330372
## Run 11 stress 0.1797572
## ... Procrustes: rmse 0.01798144 max resid 0.1116487
## Run 12 stress 0.1888051
## Run 13 stress 0.1840194
## Run 14 stress 0.1811201
## Run 15 stress 0.1804232
## Run 16 stress 0.1796063
## ... Procrustes: rmse 0.01256045 max resid 0.1082769
## Run 17 stress 0.1806517
## Run 18 stress 0.1832335
## Run 19 stress 0.1804368
## Run 20 stress 0.1853824
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 18: no. of iterations >= maxit
## 2: stress ratio > sratmaxmetaMDS(its2.asv.hell, k=3, previous.best = its2.mds.hell.3)## Starting from 3-dimensional configuration
## Run 0 stress 0.1795205
## Run 1 stress 0.1827519
## Run 2 stress 0.1798022
## ... Procrustes: rmse 0.01582041 max resid 0.09598276
## Run 3 stress 0.1803149
## Run 4 stress 0.1848867
## Run 5 stress 0.1819429
## Run 6 stress 0.1796089
## ... Procrustes: rmse 0.0126113 max resid 0.1046857
## Run 7 stress 0.1803114
## Run 8 stress 0.1796505
## ... Procrustes: rmse 0.01363958 max resid 0.1047757
## Run 9 stress 0.1795696
## ... Procrustes: rmse 0.006330195 max resid 0.06301324
## Run 10 stress 0.1837267
## Run 11 stress 0.1841725
## Run 12 stress 0.1850958
## Run 13 stress 0.1876756
## Run 14 stress 0.1827281
## Run 15 stress 0.1802518
## Run 16 stress 0.1849083
## Run 17 stress 0.1819602
## Run 18 stress 0.1846738
## Run 19 stress 0.1801131
## Run 20 stress 0.1822352
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 18: no. of iterations >= maxit
## 2: stress ratio > sratmax##
## Call:
## metaMDS(comm = its2.asv.hell, k = 3, previous.best = its2.mds.hell.3)
##
## global Multidimensional Scaling using monoMDS
##
## Data: its2.asv.hell
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1795205
## Stress type 1, weak ties
## Best solution was not repeated after 40 tries
## The best solution was from try 0 (metric scaling or null solution)
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'its2.asv.hell'its2.mds.prop <- metaMDS(its2.asv.prop)## Run 0 stress 0.2014211
## Run 1 stress 0.2107384
## Run 2 stress 0.2096602
## Run 3 stress 0.2135925
## Run 4 stress 0.2086454
## Run 5 stress 0.2154752
## Run 6 stress 0.2125952
## Run 7 stress 0.2060756
## Run 8 stress 0.2050126
## Run 9 stress 0.209379
## Run 10 stress 0.2165897
## Run 11 stress 0.2087148
## Run 12 stress 0.2091691
## Run 13 stress 0.2155498
## Run 14 stress 0.223542
## Run 15 stress 0.2089512
## Run 16 stress 0.2076853
## Run 17 stress 0.2071709
## Run 18 stress 0.2181931
## Run 19 stress 0.2086439
## Run 20 stress 0.2098481
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 7: no. of iterations >= maxit
## 13: stress ratio > sratmaxits2.mds.prop.3 <- metaMDS(its2.asv.prop, k=3)## Run 0 stress 0.1501586
## Run 1 stress 0.1499261
## ... New best solution
## ... Procrustes: rmse 0.04452019 max resid 0.2160773
## Run 2 stress 0.1501838
## ... Procrustes: rmse 0.04517297 max resid 0.2398887
## Run 3 stress 0.1506645
## Run 4 stress 0.150633
## Run 5 stress 0.1496062
## ... New best solution
## ... Procrustes: rmse 0.02365725 max resid 0.2072309
## Run 6 stress 0.1506949
## Run 7 stress 0.1499125
## ... Procrustes: rmse 0.04418184 max resid 0.239235
## Run 8 stress 0.1535526
## Run 9 stress 0.1547474
## Run 10 stress 0.1542647
## Run 11 stress 0.1503214
## Run 12 stress 0.1562014
## Run 13 stress 0.1529133
## Run 14 stress 0.1520036
## Run 15 stress 0.150364
## Run 16 stress 0.1536149
## Run 17 stress 0.1506543
## Run 18 stress 0.1534635
## Run 19 stress 0.1570662
## Run 20 stress 0.1543156
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 15: no. of iterations >= maxit
## 5: stress ratio > sratmaxnmds.its2=metaMDS(its2.asv.prop, k=3, previous.best = its2.mds.prop.3)## Starting from 3-dimensional configuration
## Run 0 stress 0.1496062
## Run 1 stress 0.1499121
## ... Procrustes: rmse 0.03875206 max resid 0.2443582
## Run 2 stress 0.1542449
## Run 3 stress 0.1506679
## Run 4 stress 0.151191
## Run 5 stress 0.1546472
## Run 6 stress 0.1541318
## Run 7 stress 0.1502279
## Run 8 stress 0.1508227
## Run 9 stress 0.1553195
## Run 10 stress 0.1496495
## ... Procrustes: rmse 0.003538382 max resid 0.03443763
## Run 11 stress 0.1509365
## Run 12 stress 0.1511187
## Run 13 stress 0.1533337
## Run 14 stress 0.1520943
## Run 15 stress 0.1513405
## Run 16 stress 0.1504105
## Run 17 stress 0.1513908
## Run 18 stress 0.1508853
## Run 19 stress 0.1516135
## Run 20 stress 0.1510949
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 17: no. of iterations >= maxit
## 3: stress ratio > sratmax#site scores
data.scores.its2 <- as.data.frame(scores(nmds.its2)$sites) #Using the scores function from vegan to extract the site scores and convert to a data.frame
data.scores.its2$site <- rownames(data.scores.its2) # create a column of site names, from the rownames of data.scores
data.scores.its2=full_join(data.scores.its2, meta)## Joining with `by = join_by(site)`#species scores
species.scores.its2 <- as.data.frame(scores(nmds.its2, "species")) #Using the scores function from vegan to extract the species scores and convert to a data.frame
species.scores.its2$species <- rownames(species.scores.its2) # create a column of species, from the rownames of species.scoresits2.A=ggplot(data= data.scores.its2,aes(x=NMDS1,y=NMDS2,shape= CO2,colour=CO2)) +
#geom_text(data=species.scores.its2,aes(x=NMDS1,y=NMDS2,label=species),alpha=0.5) + # add the species labels
geom_point(size=3) + # add the point markers
#geom_text(data=data.scores.its2,aes(x=NMDS1,y=NMDS2,label=site),size=6,vjust=0) + # add the site labels
scale_colour_manual(values=c("Elevated" = "red", "Control" = "blue")) +
coord_equal() +
theme_bw()+
guides(color=guide_legend(expression(paste("CO"["2"]))), shape = FALSE)
#axis 1 v 3
if("NMDS3" %in% colnames(data.scores.its2) ==TRUE){
its2.B=ggplot(data= data.scores.its2,aes(x=NMDS1,y=NMDS3,shape= CO2,colour=CO2)) +
#geom_text(data=species.scores.its2,aes(x=NMDS1,y=NMDS2,label=species),alpha=0.5) + # add the species labels
geom_point(size=3) + # add the point markers
#geom_text(data=data.scores.its2,aes(x=NMDS1,y=NMDS2,label=site),size=6,vjust=0) + # add the site labels
scale_colour_manual(values=c("Elevated" = "red", "Control" = "blue")) +
coord_equal() +
theme_bw()+
guides(color=guide_legend(expression(paste("CO"["2"]))), shape = FALSE)
}
#axis 2 vs 3
if("NMDS3" %in% colnames(data.scores.its2) ==TRUE){
its2.C=ggplot(data= data.scores.its2,aes(x=NMDS2,y=NMDS3,shape= CO2,colour=CO2)) +
#geom_text(data=species.scores.its2,aes(x=NMDS1,y=NMDS2,label=species),alpha=0.5) + # add the species labels
geom_point(size=3) + # add the point markers
#geom_text(data=data.scores.its2,aes(x=NMDS1,y=NMDS2,label=site),size=6,vjust=0) + # add the site labels
scale_colour_manual(values=c("Elevated" = "red", "Control" = "blue")) +
coord_equal() +
theme_bw()+
guides(color=guide_legend(expression(paste("CO"["2"]))), shape = FALSE)
}
its2.all= its2.A + its2.B + its2.CBacteria
# NMDS
bacteria.mds.hell <- metaMDS(bacteria.asv.hell)## Run 0 stress 0.2129363
## Run 1 stress 0.2331149
## Run 2 stress 0.2365677
## Run 3 stress 0.2249617
## Run 4 stress 0.2205346
## Run 5 stress 0.2220319
## Run 6 stress 0.2113902
## ... New best solution
## ... Procrustes: rmse 0.02221691 max resid 0.1556173
## Run 7 stress 0.2168891
## Run 8 stress 0.2211196
## Run 9 stress 0.2130616
## Run 10 stress 0.2305469
## Run 11 stress 0.229972
## Run 12 stress 0.2302245
## Run 13 stress 0.2254145
## Run 14 stress 0.2295191
## Run 15 stress 0.219298
## Run 16 stress 0.2118241
## ... Procrustes: rmse 0.01711956 max resid 0.1641574
## Run 17 stress 0.2347548
## Run 18 stress 0.2113892
## ... New best solution
## ... Procrustes: rmse 0.005853489 max resid 0.06050097
## Run 19 stress 0.2193599
## Run 20 stress 0.2113683
## ... New best solution
## ... Procrustes: rmse 0.005833782 max resid 0.06067458
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 2: no. of iterations >= maxit
## 18: stress ratio > sratmaxbacteria.mds.hell.3 <- metaMDS(bacteria.asv.hell, k=3)## Run 0 stress 0.1579925
## Run 1 stress 0.158922
## Run 2 stress 0.1578357
## ... New best solution
## ... Procrustes: rmse 0.02803642 max resid 0.1370321
## Run 3 stress 0.1579638
## ... Procrustes: rmse 0.04761142 max resid 0.1523802
## Run 4 stress 0.1604293
## Run 5 stress 0.1575072
## ... New best solution
## ... Procrustes: rmse 0.04638111 max resid 0.1543406
## Run 6 stress 0.1583354
## Run 7 stress 0.1581992
## Run 8 stress 0.1588536
## Run 9 stress 0.158729
## Run 10 stress 0.1573232
## ... New best solution
## ... Procrustes: rmse 0.01089757 max resid 0.0766522
## Run 11 stress 0.1579875
## Run 12 stress 0.1583026
## Run 13 stress 0.157214
## ... New best solution
## ... Procrustes: rmse 0.04014039 max resid 0.1455551
## Run 14 stress 0.1578314
## Run 15 stress 0.1618956
## Run 16 stress 0.160168
## Run 17 stress 0.1598794
## Run 18 stress 0.1600597
## Run 19 stress 0.1572211
## ... Procrustes: rmse 0.04075845 max resid 0.1470878
## Run 20 stress 0.1619899
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 5: no. of iterations >= maxit
## 15: stress ratio > sratmaxmetaMDS(bacteria.asv.hell, k=3, previous.best = bacteria.mds.hell.3)## Starting from 3-dimensional configuration
## Run 0 stress 0.157214
## Run 1 stress 0.159564
## Run 2 stress 0.1585037
## Run 3 stress 0.1594298
## Run 4 stress 0.1570948
## ... New best solution
## ... Procrustes: rmse 0.007329505 max resid 0.06790744
## Run 5 stress 0.1580529
## Run 6 stress 0.1578176
## Run 7 stress 0.1579348
## Run 8 stress 0.1584385
## Run 9 stress 0.1600199
## Run 10 stress 0.1578467
## Run 11 stress 0.1571313
## ... Procrustes: rmse 0.00178704 max resid 0.01595673
## Run 12 stress 0.1573814
## ... Procrustes: rmse 0.0396866 max resid 0.1452538
## Run 13 stress 0.1589413
## Run 14 stress 0.1590745
## Run 15 stress 0.1572071
## ... Procrustes: rmse 0.00673171 max resid 0.06833147
## Run 16 stress 0.157541
## ... Procrustes: rmse 0.02575474 max resid 0.1366501
## Run 17 stress 0.1600043
## Run 18 stress 0.1579214
## Run 19 stress 0.1628412
## Run 20 stress 0.1581247
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 7: no. of iterations >= maxit
## 13: stress ratio > sratmax##
## Call:
## metaMDS(comm = bacteria.asv.hell, k = 3, previous.best = bacteria.mds.hell.3)
##
## global Multidimensional Scaling using monoMDS
##
## Data: bacteria.asv.hell
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1570948
## Stress type 1, weak ties
## Best solution was not repeated after 40 tries
## The best solution was from try 24 (random start)
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'bacteria.asv.hell'bacteria.mds.prop <- metaMDS(bacteria.asv.prop)## Run 0 stress 0.1627288
## Run 1 stress 0.1782991
## Run 2 stress 0.1682278
## Run 3 stress 0.1755529
## Run 4 stress 0.178149
## Run 5 stress 0.1730015
## Run 6 stress 0.1756586
## Run 7 stress 0.1698679
## Run 8 stress 0.1667112
## Run 9 stress 0.1794483
## Run 10 stress 0.1765297
## Run 11 stress 0.1689898
## Run 12 stress 0.182672
## Run 13 stress 0.1731982
## Run 14 stress 0.171074
## Run 15 stress 0.1730032
## Run 16 stress 0.1765308
## Run 17 stress 0.1629908
## ... Procrustes: rmse 0.04530894 max resid 0.4663444
## Run 18 stress 0.1775802
## Run 19 stress 0.1775409
## Run 20 stress 0.1766715
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 20: stress ratio > sratmaxbacteria.mds.prop.3 <- metaMDS(bacteria.asv.prop, k=3)## Run 0 stress 0.1129494
## Run 1 stress 0.1125481
## ... New best solution
## ... Procrustes: rmse 0.04755482 max resid 0.2724473
## Run 2 stress 0.1130145
## ... Procrustes: rmse 0.04416979 max resid 0.2683824
## Run 3 stress 0.112425
## ... New best solution
## ... Procrustes: rmse 0.05194885 max resid 0.2596961
## Run 4 stress 0.1121783
## ... New best solution
## ... Procrustes: rmse 0.02642323 max resid 0.1802529
## Run 5 stress 0.1115598
## ... New best solution
## ... Procrustes: rmse 0.04034403 max resid 0.1902641
## Run 6 stress 0.113141
## Run 7 stress 0.1135761
## Run 8 stress 0.1138553
## Run 9 stress 0.1134738
## Run 10 stress 0.1140286
## Run 11 stress 0.1118905
## ... Procrustes: rmse 0.04234992 max resid 0.2694442
## Run 12 stress 0.1112987
## ... New best solution
## ... Procrustes: rmse 0.01146419 max resid 0.11546
## Run 13 stress 0.1116482
## ... Procrustes: rmse 0.0352086 max resid 0.1347775
## Run 14 stress 0.1189774
## Run 15 stress 0.1196039
## Run 16 stress 0.1143562
## Run 17 stress 0.1143646
## Run 18 stress 0.1122263
## Run 19 stress 0.1124548
## Run 20 stress 0.1137566
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 16: no. of iterations >= maxit
## 4: stress ratio > sratmaxnmds.bac=metaMDS(bacteria.asv.hell, k=3, previous.best = bacteria.mds.hell.3)## Starting from 3-dimensional configuration
## Run 0 stress 0.157214
## Run 1 stress 0.1574495
## ... Procrustes: rmse 0.04249269 max resid 0.1481377
## Run 2 stress 0.1585958
## Run 3 stress 0.1582582
## Run 4 stress 0.1583351
## Run 5 stress 0.1595911
## Run 6 stress 0.1579867
## Run 7 stress 0.1579312
## Run 8 stress 0.1581083
## Run 9 stress 0.1572211
## ... Procrustes: rmse 0.0407458 max resid 0.1472467
## Run 10 stress 0.1579289
## Run 11 stress 0.1590843
## Run 12 stress 0.1574612
## ... Procrustes: rmse 0.04243223 max resid 0.148298
## Run 13 stress 0.1599498
## Run 14 stress 0.1587643
## Run 15 stress 0.1598681
## Run 16 stress 0.1581038
## Run 17 stress 0.157769
## Run 18 stress 0.1579328
## Run 19 stress 0.1582438
## Run 20 stress 0.157221
## ... Procrustes: rmse 0.04076249 max resid 0.1470826
## *** Best solution was not repeated -- monoMDS stopping criteria:
## 5: no. of iterations >= maxit
## 15: stress ratio > sratmax # no convergence k=2#site scores
data.scores.bac <- as.data.frame(scores(nmds.bac)$sites) #Using the scores function from vegan to extract the site scores and convert to a data.frame
data.scores.bac$site <- rownames(data.scores.bac) # create a column of site names, from the rownames of data.scores
data.scores.bac=full_join(data.scores.bac, meta)## Joining with `by = join_by(site)`#species scores
species.scores.bac <- as.data.frame(scores(nmds.bac, "species")) #Using the scores function from vegan to extract the species scores and convert to a data.frame
species.scores.bac$species <- rownames(species.scores.bac) # create a column of species, from the rownames of species.scoresbac.a=ggplot(data= data.scores.bac,aes(x=NMDS1,y=NMDS2,shape= CO2,colour=CO2)) +
#geom_text(data=species.scores.bac,aes(x=NMDS1,y=NMDS2,label=species),alpha=0.5) + # add the species labels
geom_point(size=3) + # add the point markers
#geom_text(data=data.scores.bac,aes(x=NMDS1,y=NMDS2,label=site),size=6,vjust=0) + # add the site labels
scale_colour_manual(values=c("Elevated" = "red", "Control" = "blue"), labels= c("Elevated", "Ambient")) +
coord_equal() +
theme_bw()+
guides(color=guide_legend(expression(paste("CO"["2"]))), shape = FALSE)
#axis 1 v 3
if("NMDS3" %in% colnames(data.scores.bac) ==TRUE){
bac.b=ggplot(data= data.scores.bac,aes(x=NMDS1,y=NMDS3,shape= CO2,colour=CO2)) +
#geom_text(data=species.scores.bac,aes(x=NMDS1,y=NMDS2,label=species),alpha=0.5) + # add the species labels
geom_point(size=3) + # add the point markers
#geom_text(data=data.scores.bac,aes(x=NMDS1,y=NMDS2,label=site),size=6,vjust=0) + # add the site labels
scale_colour_manual(values=c("Elevated" = "red", "Control" = "blue")) +
coord_equal() +
theme_bw()+
guides(color=guide_legend(expression(paste("CO"["2"]))), shape = FALSE)
}
#axis 2 vs 3
if("NMDS3" %in% colnames(data.scores.bac) ==TRUE){
bac.c= ggplot(data= data.scores.bac,aes(x=NMDS2,y=NMDS3,shape= CO2,colour=CO2)) +
#geom_text(data=species.scores.bac,aes(x=NMDS1,y=NMDS2,label=species),alpha=0.5) + # add the species labels
geom_point(size=3) + # add the point markers
#geom_text(data=data.scores.bac,aes(x=NMDS1,y=NMDS2,label=site),size=6,vjust=0) + # add the site labels
scale_colour_manual(values=c("Elevated" = "red", "Control" = "blue")) +
coord_equal() +
theme_bw()+
guides(color=guide_legend(expression(paste("CO"["2"]))), shape = FALSE)
}
bac.all= bac.a + bac.b + bac.cFig 1: multiplot fungi and bacterial
its2.A.noleg= its2.A + theme(legend.position = "none") + geom_label(aes(x = 0.3, y = 1.5, label = "Fungal composition"), inherit.aes = F)
bac.a.bot= bac.a + theme(legend.position = "bottom") + geom_label(aes(x = -.2, y = 1, label = "Bacterial composition"), inherit.aes = F) + expand_limits(x = 0.7, y= 1.2)
fig1.vertical= its2.A.noleg / bac.a.bot
ggsave(paste0(output.loc, "/fig.1.pdf"), fig1.vertical, width = 6)## Saving 6 x 5 in imageggsave(paste0(output.loc, "/fig.1.jpg"), fig1.vertical, width = 6)## Saving 6 x 5 in image4.2.1 Stats
ITS1
# plot 20_9 doesn't appear to be in the ASV tab and is blank in the meta tab
meta.fin=meta %>%
filter(site !="20_9")
adonmod=adonis2(ITS1.asv.hell ~ CO2, data = meta.fin)
# check for dispersion
#use data.scores df to get corresponding treatment assignments in proper order
treatment= data.scores.its1 %>%
filter(site!= "20_9")
dis.its1= vegdist(ITS1.asv.hell)
mod <- betadisper(dis.its1, treatment$CO2)
anova(mod)(mod.HSD <- TukeyHSD(mod))## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = distances ~ group, data = df)
##
## $group
## diff lwr upr p adj
## Elevated-Control 0.007349717 -0.02828053 0.04297996 0.683596plot(mod.HSD)
its2
adonmod_ITS2=adonis2(its2.asv.prop ~ CO2, data = meta.fin)
# check for dispersion
#use data.scores df to get corresponding treatment assignments in proper order
treatment= data.scores.its2 %>%
filter(site!= "20_9")
dis= vegdist(its2.asv.prop)
mod <- betadisper(dis, treatment$CO2)
anova(mod)(mod.HSD <- TukeyHSD(mod))## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = distances ~ group, data = df)
##
## $group
## diff lwr upr p adj
## Elevated-Control 0.009565556 -0.03537924 0.05451035 0.6741235plot(mod.HSD)
Bacteria
# adonis
adonmod_16s=adonis2(bacteria.asv.hell ~ CO2, data = meta.fin)
# check for dispersion
#use data.scores df to get corresponding treatment assignments in proper order
treatment= data.scores.bac %>%
filter(site!= "20-9")
dis= vegdist(bacteria.asv.hell)
mod <- betadisper(dis, treatment$CO2)
anova(mod)(mod.HSD <- TukeyHSD(mod))## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = distances ~ group, data = df)
##
## $group
## diff lwr upr p adj
## Elevated-Control 0.01786205 -0.02857368 0.06429777 0.4476551plot(mod.HSD)
5 NETWORKS
- Filtering low abundant ASVs, maintaining ASVs with more than 10 read counts
Remove low abundant ASVs
# ITS1
its1.net= its1.net %>% column_to_rownames("Sample")
its1.sub=its1.net[ ,colSums(its1.net[,1:ncol(its1.net)]) >= 10]
paste("filtering low abundant ASVs removes", ncol(its1.net)- ncol(its1.sub), "ASVs")## [1] "filtering low abundant ASVs removes 25 ASVs"# its2
its2.net= its2.net %>% column_to_rownames("Sample")
its2.sub=its2.net[ ,colSums(its2.net[,1:ncol(its2.net)]) >= 10]
paste("filtering low abundant ASVs removes", ncol(its2.net)- ncol(its2.sub), "ASVs")## [1] "filtering low abundant ASVs removes 36 ASVs"# 16s
bac.net= bac.net %>% column_to_rownames("Sample")
bac.sub=bac.net[ ,colSums(bac.net[,2:ncol(bac.net)]) >= 10]
paste("filtering low abundant ASVs removes", ncol(bac.net)- ncol(bac.sub), "ASVs")## [1] "filtering low abundant ASVs removes 23 ASVs"Filter all.tax by the filtered asv tables
its1.sub.vec= names(its1.sub)
its1.tax.sub= its1.tax %>%
filter(uniqueID %in% its1.sub.vec)
its2.sub.vec= names(its2.sub)
its2.tax.sub= its2.tax %>%
filter(uniqueID %in% its2.sub.vec)
bac.sub.vec= names(bac.sub)
bac.tax.sub= bac.tax %>%
filter(uniqueID %in% bac.sub.vec)Split Elevated CO2 and Ambient
Combine 3 asv dfs into a list item
# all.asvs= list(ITS1.asv.filter, its2.asv.filter, bacteria.asv.tab.filter) #old
all.asvs= list(its1.sub, its2.sub, bac.sub)
names(all.asvs)<- c("its1", "its2", "16s")
# all.tax= list(its1.tax, its2.tax, bac.tax) #old
all.tax= list(its1.tax.sub, its2.tax.sub, bac.tax.sub)
names(all.tax)<- c("its1", "its2", "16s")# make a col named sample to link metadata in
all.asvs=all.asvs %>%
map(rownames_to_column, "Sample")
# add metadata
meta$site= sub("_", "-", meta$site)
meta.lite= meta %>%
select(site, CO2) %>%
rename(Sample= site)
all.asvs= all.asvs %>%
map(full_join, meta.lite) %>% # add metadata to asv data so we know which Samples are Elevated and which are Control
map(relocate, "CO2", .after= "Sample") # move co2 treatment to start of df for each so we can see it## Joining with `by = join_by(Sample)`
## Joining with `by = join_by(Sample)`
## Joining with `by = join_by(Sample)`Elevated=all.asvs %>%
map(filter, CO2 == "Elevated") %>%
map(select, -c(CO2)) %>%
map( column_to_rownames, "Sample")
# Elevated[1] # check to see if that worked
Elevated[3]## $`16s`
## Methylobacterium-Methylorubrum sp. Methylobacterium-Methylorubrum sp..1
## 20-10 2315 9
## 20-11 540 0
## 20-12 324 0
## 20-13 144 715
## 20-14 19 1291
## 20-15 289 0
## 20-2 1123 6
## 20-3 3957 546
## 20-4 2433 419
## 20-5 3374 0
## 20-6 949 196
## 20-7 1171 0
## 20-8 229 96
## 21-1 0 0
## 21-10 2357 0
## 21-11 728 365
## 21-12 0 433
## 21-13 1119 153
## 21-14 1401 0
## 21-15 0 0
## 21-2 0 12
## 21-3 1027 0
## 21-4 1728 0
## 21-5 2125 0
## 21-6 532 170
## 21-7 2534 0
## 21-8 539 0
## 21-9 46 5
## 28-1 14 80
## 28-10 625 16
## 28-11 851 1008
## 28-12 1987 8
## 28-13 3117 0
## 28-14 4430 0
## 28-15 2629 286
## 28-2 1622 139
## 28-3 2263 0
## 28-4 1257 0
## 28-5 72 208
## 28-6 2938 24
## 28-7 956 131
## 28-8 840 0
## 28-9 3037 0
## 29-1 2265 572
## 29-10 0 1316
## 29-11 3637 0
## 29-12 237 853
## 29-13 1664 2219
## 29-14 4051 356
## 29-15 38 822
## 29-2 1553 37
## 29-3 785 0
## 29-4 1749 0
## 29-5 29 629
## 29-6 1574 311
## 29-7 1814 3066
## 29-8 910 342
## 29-9 301 0
## Sphingomonas cynarae Aureimonas sp. Escherichia-Shigella sp.
## 20-10 1823 50 0
## 20-11 0 86 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 102 14 0
## 20-15 0 0 0
## 20-2 209 276 0
## 20-3 0 16 0
## 20-4 0 0 0
## 20-5 340 0 156
## 20-6 196 78 0
## 20-7 753 206 0
## 20-8 0 0 0
## 21-1 331 17 35
## 21-10 107 0 0
## 21-11 200 209 15
## 21-12 0 0 473
## 21-13 23 114 0
## 21-14 0 655 153
## 21-15 0 0 37
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 796
## 21-6 0 78 0
## 21-7 157 0 156
## 21-8 146 0 0
## 21-9 0 0 0
## 28-1 0 0 65
## 28-10 108 0 0
## 28-11 38 0 0
## 28-12 34 0 0
## 28-13 41 441 0
## 28-14 0 950 0
## 28-15 36 287 249
## 28-2 21 100 0
## 28-3 678 159 43
## 28-4 0 42 254
## 28-5 0 201 242
## 28-6 52 537 0
## 28-7 46 186 45
## 28-8 172 972 0
## 28-9 0 0 1085
## 29-1 75 328 0
## 29-10 0 0 1174
## 29-11 61 14 17
## 29-12 168 16 0
## 29-13 574 535 54
## 29-14 0 192 0
## 29-15 0 0 0
## 29-2 193 256 0
## 29-3 0 112 257
## 29-4 275 242 0
## 29-5 184 497 0
## 29-6 82 240 0
## 29-7 115 199 0
## 29-8 138 149 0
## 29-9 0 0 0
## Quadrisphaera granulorum Aureimonas sp..1 Klenkia sp.
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 993 0 892
## 20-14 112 0 29
## 20-15 0 0 0
## 20-2 24 0 0
## 20-3 158 0 0
## 20-4 140 0 0
## 20-5 238 215 0
## 20-6 0 0 51
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 10 0 55
## 21-10 39 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 26
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 30 20 33
## 21-4 257 19 11
## 21-5 34 0 0
## 21-6 0 35 190
## 21-7 51 312 6
## 21-8 52 0 29
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 14 0 0
## 28-12 0 93 372
## 28-13 0 41 0
## 28-14 62 52 0
## 28-15 215 0 0
## 28-2 0 0 88
## 28-3 0 0 0
## 28-4 131 54 0
## 28-5 315 0 39
## 28-6 0 17 0
## 28-7 0 0 17
## 28-8 0 36 5
## 28-9 0 0 0
## 29-1 131 0 0
## 29-10 0 0 0
## 29-11 5 699 0
## 29-12 0 0 0
## 29-13 292 33 87
## 29-14 144 85 128
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 673 0
## 29-4 166 35 5
## 29-5 68 0 29
## 29-6 0 0 0
## 29-7 33 356 114
## 29-8 122 62 9
## 29-9 6 0 0
## Pseudokineococcus lusitanus Methylobacterium-Methylorubrum sp..2
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 56 0
## 20-14 64 1011
## 20-15 0 0
## 20-2 0 0
## 20-3 160 0
## 20-4 0 0
## 20-5 55 0
## 20-6 0 0
## 20-7 193 0
## 20-8 0 0
## 21-1 0 0
## 21-10 380 0
## 21-11 27 0
## 21-12 0 0
## 21-13 45 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 30 0
## 21-4 31 0
## 21-5 0 0
## 21-6 599 236
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 42 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 96 0
## 29-10 0 0
## 29-11 0 0
## 29-12 49 0
## 29-13 15 300
## 29-14 75 197
## 29-15 0 0
## 29-2 0 0
## 29-3 346 0
## 29-4 33 0
## 29-5 0 0
## 29-6 58 0
## 29-7 0 0
## 29-8 32 0
## 29-9 32 0
## Aureimonas populi Sphingomonas sp. Methylobacterium-Methylorubrum sp..3
## 20-10 0 0 0
## 20-11 0 0 185
## 20-12 0 4 16
## 20-13 42 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 108 259 519
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 65
## 21-10 164 338 0
## 21-11 122 26 0
## 21-12 0 0 0
## 21-13 0 26 16
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 329 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 123 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 39 0
## 28-10 0 68 0
## 28-11 0 16 0
## 28-12 0 0 0
## 28-13 0 0 19
## 28-14 0 0 0
## 28-15 50 81 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 112 92 0
## 28-5 0 48 0
## 28-6 133 0 0
## 28-7 21 0 0
## 28-8 163 51 0
## 28-9 0 56 0
## 29-1 18 36 29
## 29-10 0 0 0
## 29-11 29 225 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 398 165 0
## 29-15 0 0 0
## 29-2 0 34 88
## 29-3 0 94 0
## 29-4 0 74 161
## 29-5 0 36 0
## 29-6 0 0 0
## 29-7 0 14 0
## 29-8 0 94 0
## 29-9 0 0 0
## Methylobacterium-Methylorubrum sp..4 Aurantimonas sp.
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 213
## 20-4 0 0
## 20-5 0 54
## 20-6 0 0
## 20-7 0 101
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 9
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 32
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 69
## 29-10 0 210
## 29-11 0 0
## 29-12 0 0
## 29-13 0 150
## 29-14 0 56
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 47
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 18
## Methylobacterium-Methylorubrum sp..5 Methylobacterium-Methylorubrum sp..6
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 923
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..7 Sphingomonas mucosissima
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 47
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 341
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 24 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 394
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 59 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Bdellovibrio sp. Methylobacterium-Methylorubrum sp..8 Quadrisphaera sp.
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 36 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 389 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 22 0 0
## 29-9 0 0 0
## Hymenobacter rivuli Methylobacterium-Methylorubrum sp..9
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 545
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 281 0
## 29-8 0 0
## 29-9 0 0
## Aurantimonas sp..1 Methylobacterium-Methylorubrum sp..10
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 346
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Sphingomonas sp..1 Methylobacterium-Methylorubrum sp..11 Hymenobacter sp.
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 10
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 324 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 78
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 235
## 29-8 0 0 0
## 29-9 0 0 0
## Escherichia-Shigella sp..1 Aureimonas sp..2
## 20-10 0 0
## 20-11 0 0
## 20-12 0 275
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..12 Herbiconiux sp. Oscillatoria sp.
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 124 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 50 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Microbacterium sp. Methylobacterium-Methylorubrum sp..13
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 8 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 244
## 20-4 0 0
## 20-5 68 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 13 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 51 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 7 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Hymenobacter sp..1 Aureimonas sp..3 Sphingomonas sp..2
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 70
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 114
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 243 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Methylobacterium-Methylorubrum sp..14
## 20-10 0
## 20-11 0
## 20-12 0
## 20-13 0
## 20-14 0
## 20-15 0
## 20-2 0
## 20-3 0
## 20-4 0
## 20-5 0
## 20-6 0
## 20-7 0
## 20-8 0
## 21-1 0
## 21-10 0
## 21-11 0
## 21-12 0
## 21-13 0
## 21-14 0
## 21-15 0
## 21-2 0
## 21-3 0
## 21-4 0
## 21-5 0
## 21-6 0
## 21-7 0
## 21-8 0
## 21-9 0
## 28-1 0
## 28-10 0
## 28-11 0
## 28-12 0
## 28-13 0
## 28-14 0
## 28-15 0
## 28-2 0
## 28-3 0
## 28-4 0
## 28-5 0
## 28-6 0
## 28-7 0
## 28-8 0
## 28-9 0
## 29-1 0
## 29-10 0
## 29-11 0
## 29-12 0
## 29-13 199
## 29-14 0
## 29-15 0
## 29-2 0
## 29-3 0
## 29-4 0
## 29-5 0
## 29-6 0
## 29-7 0
## 29-8 0
## 29-9 0
## Methylobacterium-Methylorubrum sp..15 Aureimonas sp..4 Hymenobacter sp..2
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 194 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 10
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 130
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Ensifer sp. Methylobacterium-Methylorubrum sp..16 Oscillatoria sp..1
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 99 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 26 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 182 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Marmoricola sp. Methylobacterium-Methylorubrum sp..17
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 168 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..18 Hymenobacter sp..3
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 162
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 166 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Sphingomonas sp..3 Oscillatoria sp..2
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 153 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..19
## 20-10 0
## 20-11 0
## 20-12 0
## 20-13 0
## 20-14 0
## 20-15 0
## 20-2 0
## 20-3 0
## 20-4 0
## 20-5 0
## 20-6 0
## 20-7 0
## 20-8 0
## 21-1 0
## 21-10 0
## 21-11 151
## 21-12 0
## 21-13 0
## 21-14 0
## 21-15 0
## 21-2 0
## 21-3 0
## 21-4 0
## 21-5 0
## 21-6 0
## 21-7 0
## 21-8 0
## 21-9 0
## 28-1 0
## 28-10 0
## 28-11 0
## 28-12 0
## 28-13 0
## 28-14 0
## 28-15 0
## 28-2 0
## 28-3 0
## 28-4 0
## 28-5 0
## 28-6 0
## 28-7 0
## 28-8 0
## 28-9 0
## 29-1 0
## 29-10 0
## 29-11 0
## 29-12 0
## 29-13 0
## 29-14 0
## 29-15 0
## 29-2 0
## 29-3 0
## 29-4 0
## 29-5 0
## 29-6 0
## 29-7 0
## 29-8 0
## 29-9 0
## Methylobacterium-Methylorubrum sp..20 Oscillatoria sp..3
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 151 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Sphingomonas sp..4 Oscillatoria sp..4
## 20-10 0 141
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 47 0
## 29-12 0 0
## 29-13 0 0
## 29-14 30 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 33 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..21 Thermus sp.
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 139 0
## 20-5 0 0
## 20-6 0 136
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..22
## 20-10 0
## 20-11 0
## 20-12 0
## 20-13 0
## 20-14 0
## 20-15 0
## 20-2 0
## 20-3 0
## 20-4 0
## 20-5 0
## 20-6 0
## 20-7 0
## 20-8 0
## 21-1 0
## 21-10 0
## 21-11 0
## 21-12 0
## 21-13 0
## 21-14 0
## 21-15 0
## 21-2 0
## 21-3 0
## 21-4 0
## 21-5 136
## 21-6 0
## 21-7 0
## 21-8 0
## 21-9 0
## 28-1 0
## 28-10 0
## 28-11 0
## 28-12 0
## 28-13 0
## 28-14 0
## 28-15 0
## 28-2 0
## 28-3 0
## 28-4 0
## 28-5 0
## 28-6 0
## 28-7 0
## 28-8 0
## 28-9 0
## 29-1 0
## 29-10 0
## 29-11 0
## 29-12 0
## 29-13 0
## 29-14 0
## 29-15 0
## 29-2 0
## 29-3 0
## 29-4 0
## 29-5 0
## 29-6 0
## 29-7 0
## 29-8 0
## 29-9 0
## Methylobacterium-Methylorubrum sp..23 Quadrisphaera sp..1
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 135 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..24 Acinetobacter sp.
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 130
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 133 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..25
## 20-10 0
## 20-11 0
## 20-12 0
## 20-13 0
## 20-14 0
## 20-15 0
## 20-2 0
## 20-3 0
## 20-4 0
## 20-5 0
## 20-6 0
## 20-7 0
## 20-8 0
## 21-1 0
## 21-10 0
## 21-11 0
## 21-12 0
## 21-13 0
## 21-14 0
## 21-15 0
## 21-2 0
## 21-3 0
## 21-4 0
## 21-5 0
## 21-6 0
## 21-7 0
## 21-8 0
## 21-9 0
## 28-1 0
## 28-10 0
## 28-11 0
## 28-12 0
## 28-13 0
## 28-14 0
## 28-15 0
## 28-2 0
## 28-3 0
## 28-4 0
## 28-5 0
## 28-6 0
## 28-7 0
## 28-8 0
## 28-9 0
## 29-1 0
## 29-10 0
## 29-11 0
## 29-12 0
## 29-13 0
## 29-14 128
## 29-15 0
## 29-2 0
## 29-3 0
## 29-4 0
## 29-5 0
## 29-6 0
## 29-7 0
## 29-8 0
## 29-9 0
## Methylobacterium-Methylorubrum sp..26 Oscillatoria sp..5
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..27
## 20-10 0
## 20-11 0
## 20-12 0
## 20-13 0
## 20-14 0
## 20-15 0
## 20-2 0
## 20-3 0
## 20-4 0
## 20-5 0
## 20-6 0
## 20-7 0
## 20-8 0
## 21-1 0
## 21-10 0
## 21-11 0
## 21-12 0
## 21-13 0
## 21-14 0
## 21-15 0
## 21-2 0
## 21-3 0
## 21-4 0
## 21-5 0
## 21-6 0
## 21-7 0
## 21-8 0
## 21-9 0
## 28-1 0
## 28-10 0
## 28-11 0
## 28-12 0
## 28-13 0
## 28-14 0
## 28-15 0
## 28-2 0
## 28-3 0
## 28-4 0
## 28-5 0
## 28-6 0
## 28-7 0
## 28-8 0
## 28-9 0
## 29-1 0
## 29-10 0
## 29-11 0
## 29-12 0
## 29-13 0
## 29-14 0
## 29-15 0
## 29-2 0
## 29-3 0
## 29-4 0
## 29-5 0
## 29-6 0
## 29-7 0
## 29-8 0
## 29-9 0
## Methylobacterium-Methylorubrum sp..28 Oscillatoria sp..6
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 109
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Sphingomonas sp..5 Oscillatoria sp..7 Pseudomonas sp.
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 107 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 91
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Pseudokineococcus sp. Oscillatoria sp..8 Ensifer sp..1
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 100
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Escherichia-Shigella sp..2 Methylobacterium-Methylorubrum sp..29
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 96
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Oscillatoria sp..9 Methylobacterium-Methylorubrum sp..30
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 96 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 96
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Novosphingobium sp. Methylobacterium-Methylorubrum sp..31
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 91
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Escherichia-Shigella sp..3 Oscillatoria sp..10
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 85
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..32 Neorhizobium sp. Sphingomonas sp..6
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 80
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Hymenobacter sp..4 Methylobacterium-Methylorubrum sp..33
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 9 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 16 0
## 29-8 0 0
## 29-9 0 0
## Oscillatoria sp..11 Methylobacterium-Methylorubrum sp..34
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 76
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Sphingomonas sp..7 Methylobacterium-Methylorubrum sp..35
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 75 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Hymenobacter sp..5 Rathayibacter sp.
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 13
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 59
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 74 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..36 Oscillatoria sp..12 Erwiniaceae
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 71 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 67
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Aureimonas sp..5 Oscillatoria sp..13
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 66 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..37 Roseomonas sp. Quadrisphaera sp..2
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 64 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 32 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Roseomonas sp..1 Sphingomonas sp..8 Oscillatoria sp..14
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Rhodocytophaga sp. Oscillatoria sp..15 Aurantimonas sp..2
## 20-10 61 61 60
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Granulicatella elegans Aureimonas sp..6 Sphingomonas sp..9
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 59
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 60 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Kineococcus sp. Escherichia-Shigella sp..4 Oscillatoria sp..16
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 58 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Oscillatoria sp..17 Methylobacterium-Methylorubrum sp..38
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 57 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 54
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Oscillatoria sp..18 Methylobacterium-Methylorubrum sp..39
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 53
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Aureimonas sp..7 Staphylococcus sp. Aureimonas sp..8 Enterobacteriaceae
## 20-10 0 0 0 0
## 20-11 0 0 0 0
## 20-12 0 0 0 0
## 20-13 0 0 0 0
## 20-14 0 0 0 0
## 20-15 0 0 0 0
## 20-2 0 0 0 0
## 20-3 0 0 0 0
## 20-4 0 0 0 0
## 20-5 0 0 0 0
## 20-6 0 0 0 0
## 20-7 0 0 0 0
## 20-8 0 0 0 0
## 21-1 0 0 0 0
## 21-10 0 0 0 0
## 21-11 0 0 0 0
## 21-12 0 0 0 0
## 21-13 0 0 0 0
## 21-14 0 0 0 0
## 21-15 0 0 0 0
## 21-2 0 0 0 0
## 21-3 0 0 0 0
## 21-4 0 0 0 0
## 21-5 0 0 0 0
## 21-6 0 0 0 0
## 21-7 0 0 0 0
## 21-8 0 0 0 0
## 21-9 0 0 0 0
## 28-1 0 0 0 0
## 28-10 0 0 0 0
## 28-11 0 0 51 0
## 28-12 0 0 0 0
## 28-13 0 0 0 0
## 28-14 0 0 0 0
## 28-15 52 0 0 0
## 28-2 0 0 0 0
## 28-3 0 0 0 0
## 28-4 0 25 0 0
## 28-5 0 0 0 0
## 28-6 0 0 0 0
## 28-7 0 0 0 0
## 28-8 0 0 0 0
## 28-9 0 0 0 0
## 29-1 0 0 0 0
## 29-10 0 0 0 0
## 29-11 0 0 0 0
## 29-12 0 0 0 0
## 29-13 0 0 0 0
## 29-14 0 0 0 0
## 29-15 0 0 0 0
## 29-2 0 0 0 0
## 29-3 0 0 0 0
## 29-4 0 0 0 0
## 29-5 0 0 0 0
## 29-6 0 0 0 0
## 29-7 0 0 0 0
## 29-8 0 0 0 0
## 29-9 0 0 0 0
## Oscillatoria sp..19 Hymenobacter sp..6 Sphingomonas sp..10
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 48 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 46
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 48 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Oscillatoria sp..20 Gemmatimonadaceae Spirosoma sp. Oscillatoria sp..21
## 20-10 0 0 0 0
## 20-11 0 0 0 0
## 20-12 0 0 0 0
## 20-13 0 0 0 0
## 20-14 0 0 0 0
## 20-15 0 0 0 0
## 20-2 0 0 0 0
## 20-3 0 0 0 0
## 20-4 0 0 0 0
## 20-5 0 0 0 0
## 20-6 0 0 0 0
## 20-7 0 0 0 0
## 20-8 0 0 0 0
## 21-1 0 0 0 0
## 21-10 0 0 0 0
## 21-11 0 0 0 0
## 21-12 0 0 0 0
## 21-13 0 0 0 0
## 21-14 0 0 0 0
## 21-15 0 0 0 0
## 21-2 0 0 0 0
## 21-3 0 0 0 0
## 21-4 0 0 0 0
## 21-5 0 0 0 0
## 21-6 0 0 0 0
## 21-7 0 0 0 0
## 21-8 0 0 0 0
## 21-9 0 0 0 0
## 28-1 0 0 0 0
## 28-10 0 0 0 0
## 28-11 0 0 0 0
## 28-12 0 0 0 0
## 28-13 0 0 0 0
## 28-14 0 0 0 0
## 28-15 0 0 0 0
## 28-2 0 0 0 0
## 28-3 0 0 0 0
## 28-4 0 0 0 0
## 28-5 0 0 0 0
## 28-6 0 0 0 0
## 28-7 0 0 0 0
## 28-8 0 0 0 0
## 28-9 46 0 0 0
## 29-1 0 0 0 0
## 29-10 0 0 0 0
## 29-11 0 0 0 0
## 29-12 0 0 0 0
## 29-13 0 0 0 0
## 29-14 0 0 0 0
## 29-15 0 0 0 0
## 29-2 0 0 0 0
## 29-3 0 0 0 0
## 29-4 0 0 0 0
## 29-5 0 0 0 0
## 29-6 0 0 0 0
## 29-7 0 0 0 0
## 29-8 0 0 25 0
## 29-9 0 46 0 0
## Methylobacterium-Methylorubrum sp..40 Oscillatoria sp..22
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 44
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Oscillatoria sp..23 Oscillatoria sp..24
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..41
## 20-10 0
## 20-11 0
## 20-12 0
## 20-13 0
## 20-14 0
## 20-15 0
## 20-2 0
## 20-3 0
## 20-4 0
## 20-5 0
## 20-6 0
## 20-7 0
## 20-8 0
## 21-1 0
## 21-10 0
## 21-11 0
## 21-12 0
## 21-13 0
## 21-14 0
## 21-15 0
## 21-2 0
## 21-3 0
## 21-4 0
## 21-5 0
## 21-6 0
## 21-7 0
## 21-8 0
## 21-9 0
## 28-1 0
## 28-10 0
## 28-11 0
## 28-12 0
## 28-13 0
## 28-14 0
## 28-15 0
## 28-2 0
## 28-3 0
## 28-4 0
## 28-5 0
## 28-6 0
## 28-7 0
## 28-8 0
## 28-9 0
## 29-1 0
## 29-10 0
## 29-11 0
## 29-12 0
## 29-13 0
## 29-14 0
## 29-15 0
## 29-2 0
## 29-3 0
## 29-4 0
## 29-5 0
## 29-6 0
## 29-7 0
## 29-8 0
## 29-9 0
## Methylobacterium-Methylorubrum sp..42 Aureimonas sp..9
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 38
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 40 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Microbacterium sp..1 Oscillatoria sp..25 Ramlibacter sp.
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 37 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Aureimonas sp..10 Methylobacterium-Methylorubrum sp..43 Aureimonas sp..11
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 37 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Oscillatoria sp..26 Hymenobacter sp..7 Oscillatoria sp..27
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 33 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 34 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 33
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Oscillatoria sp..28 Oscillatoria sp..29 Quadrisphaera sp..3
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 32 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium sp.
## 20-10 0
## 20-11 0
## 20-12 0
## 20-13 0
## 20-14 0
## 20-15 0
## 20-2 0
## 20-3 0
## 20-4 0
## 20-5 0
## 20-6 0
## 20-7 0
## 20-8 0
## 21-1 0
## 21-10 0
## 21-11 0
## 21-12 0
## 21-13 0
## 21-14 0
## 21-15 0
## 21-2 0
## 21-3 0
## 21-4 0
## 21-5 0
## 21-6 0
## 21-7 0
## 21-8 0
## 21-9 0
## 28-1 0
## 28-10 0
## 28-11 0
## 28-12 0
## 28-13 0
## 28-14 0
## 28-15 0
## 28-2 0
## 28-3 0
## 28-4 0
## 28-5 0
## 28-6 0
## 28-7 0
## 28-8 0
## 28-9 0
## 29-1 0
## 29-10 0
## 29-11 0
## 29-12 0
## 29-13 0
## 29-14 0
## 29-15 0
## 29-2 0
## 29-3 0
## 29-4 0
## 29-5 0
## 29-6 0
## 29-7 0
## 29-8 0
## 29-9 0
## Oscillatoria sp..30 Methylobacterium-Methylorubrum sp..44 Klebsiella sp.
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 31 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 30
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Methylobacterium-Methylorubrum sp..45 Oscillatoria sp..31
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 29
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 30 0
## 29-8 0 0
## 29-9 0 0
## Nocardioides alpinus Methylobacterium-Methylorubrum sp..46
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 29 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 29
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Oscillatoria sp..32 Escherichia-Shigella sp..5 Oscillatoria sp..33
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 28 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 27
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Sphingomonas sp..11 Bdellovibrio sp..1
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 27 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 24
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..47 Escherichia-Shigella sp..6
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 24 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Oscillatoria sp..34 Oscillatoria sp..35 Hymenobacter sp..8
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 23 0 0
## 21-11 0 0 22
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 23 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Methylobacterium-Methylorubrum sp..48 Mesorhizobium sp.
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 22 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Oscillatoria sp..36 Pseudolabrys sp.
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Burkholderia-Caballeronia-Paraburkholderia sp. Sphingomonas sp..12
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 0
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Sphingomonas sp..13 Aureimonas sp..12 Oscillatoria sp..37
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 20 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Sphingomonas phyllosphaerae Oscillatoria sp..38 Aquamonas sp.
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 17
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 18 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 18 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Hymenobacter norwichensis Aureimonas sp..13 Brevundimonas sp.
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 6 0 0
## 29-9 0 0 0
## Escherichia-Shigella sp..7 Hymenobacter sp..9
## 20-10 0 0
## 20-11 0 0
## 20-12 0 0
## 20-13 0 0
## 20-14 0 0
## 20-15 0 0
## 20-2 0 0
## 20-3 0 0
## 20-4 0 0
## 20-5 0 0
## 20-6 0 0
## 20-7 0 0
## 20-8 0 0
## 21-1 0 0
## 21-10 0 0
## 21-11 0 0
## 21-12 0 0
## 21-13 0 0
## 21-14 0 0
## 21-15 0 0
## 21-2 0 0
## 21-3 0 0
## 21-4 0 0
## 21-5 0 0
## 21-6 0 0
## 21-7 0 0
## 21-8 0 0
## 21-9 0 0
## 28-1 0 0
## 28-10 0 0
## 28-11 0 0
## 28-12 0 0
## 28-13 0 0
## 28-14 0 0
## 28-15 0 0
## 28-2 0 0
## 28-3 0 0
## 28-4 0 0
## 28-5 0 0
## 28-6 0 0
## 28-7 0 0
## 28-8 0 0
## 28-9 0 0
## 29-1 0 0
## 29-10 0 0
## 29-11 0 0
## 29-12 0 0
## 29-13 0 0
## 29-14 0 0
## 29-15 0 0
## 29-2 0 0
## 29-3 0 0
## 29-4 0 15
## 29-5 0 0
## 29-6 0 0
## 29-7 0 0
## 29-8 0 0
## 29-9 0 0
## Methylobacterium-Methylorubrum sp..49 Salana multivorans Roseomonas sp..2
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 14 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 13 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 7
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 6
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 0 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0
## Aurantimonas sp..3 Klenkia sp..1 Klenkia sp..2
## 20-10 0 0 0
## 20-11 0 0 0
## 20-12 0 0 0
## 20-13 0 0 0
## 20-14 0 0 0
## 20-15 0 0 0
## 20-2 0 0 0
## 20-3 0 0 0
## 20-4 0 0 0
## 20-5 0 0 0
## 20-6 0 0 0
## 20-7 0 0 0
## 20-8 0 0 0
## 21-1 0 0 0
## 21-10 0 0 0
## 21-11 0 0 0
## 21-12 0 0 0
## 21-13 0 0 0
## 21-14 0 0 0
## 21-15 0 0 0
## 21-2 0 0 0
## 21-3 0 0 0
## 21-4 0 0 0
## 21-5 0 0 0
## 21-6 0 0 0
## 21-7 0 0 0
## 21-8 0 0 0
## 21-9 0 0 0
## 28-1 0 0 0
## 28-10 0 0 0
## 28-11 0 0 0
## 28-12 0 0 0
## 28-13 0 0 0
## 28-14 0 0 0
## 28-15 0 0 0
## 28-2 0 11 0
## 28-3 0 0 0
## 28-4 0 0 0
## 28-5 0 0 0
## 28-6 0 0 0
## 28-7 0 0 0
## 28-8 0 0 0
## 28-9 0 0 0
## 29-1 0 0 0
## 29-10 0 0 0
## 29-11 0 0 0
## 29-12 0 0 0
## 29-13 0 0 0
## 29-14 0 0 0
## 29-15 0 0 0
## 29-2 0 0 0
## 29-3 0 0 0
## 29-4 0 0 0
## 29-5 0 0 0
## 29-6 0 0 0
## 29-7 0 0 0
## 29-8 0 0 0
## 29-9 0 0 0Ambient=all.asvs %>%
map(filter, CO2 == "Control") %>%
map(select, -c(CO2)) %>%
map( column_to_rownames, "Sample")
# dumb way to do this, def better way to go about it. Stitch back together as a list
control.amb= c(Elevated, Ambient)
names(control.amb)<- c("elevated.its1", "elevated.its2", "elevated.16s", "amb.its1", "amb.its2", "amb.16s")Make phyloseq objects of these networks
# make phyloseq otu tables
otu= map(control.amb, otu_table, taxa_are_rows = F)
all.tax= all.tax %>%
map(.,~rownames_to_column(.x, var="seq"))
all.tax= map(all.tax, column_to_rownames,var= "uniqueID")
all.tax=map(all.tax, select, -"seq")
# duplicated these into elevated and ambient lists
Ambient.tax=all.tax
Elevated.tax=all.tax
# dumb way to do this, def better way to go about it. Stitch back together as a list
control.amb.tax= c(Elevated.tax, Ambient.tax)
names(control.amb.tax)<- c("elevated.its1", "elevated.its2", "elevated.16s", "amb.its1", "amb.its2", "amb.16s")
## make tax object
control.amb.tax= map(control.amb.tax, as.matrix)
TAX = map(control.amb.tax, tax_table)
# combine into phyloseq obj
phylo.all= map2(otu, TAX, phyloseq)5.1 Create networks via SpeicEasi
From phyloseq obj
mapply(assign, names(phylo.all), phylo.all, MoreArgs=list(envir = globalenv()))## $elevated.its1
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 397 taxa and 58 samples ]
## tax_table() Taxonomy Table: [ 397 taxa by 10 taxonomic ranks ]
##
## $elevated.its2
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1025 taxa and 58 samples ]
## tax_table() Taxonomy Table: [ 1025 taxa by 10 taxonomic ranks ]
##
## $elevated.16s
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 190 taxa and 58 samples ]
## tax_table() Taxonomy Table: [ 190 taxa by 9 taxonomic ranks ]
##
## $amb.its1
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 397 taxa and 59 samples ]
## tax_table() Taxonomy Table: [ 397 taxa by 10 taxonomic ranks ]
##
## $amb.its2
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1025 taxa and 59 samples ]
## tax_table() Taxonomy Table: [ 1025 taxa by 10 taxonomic ranks ]
##
## $amb.16s
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 190 taxa and 59 samples ]
## tax_table() Taxonomy Table: [ 190 taxa by 9 taxonomic ranks ]#its1
# gen.se.elevated.its1 <- spiec.easi(elevated.its1, method='mb', lambda.min.ratio=1e-2, nlambda=100, pulsar.params=list(rep.num=50))
#
# ## check stability
# getStability(gen.se.elevated.its1) #0.045 that seems good enough
#
# #
# gen.se.amb.its1 <- spiec.easi(amb.its1, method='mb', lambda.min.ratio=1e-2, nlambda=100, pulsar.params=list(rep.num=50))
#
# ## check stability
# getStability(gen.se.amb.its1) #0.0426
#
# #its2
# pargs2 <- list(rep.num=50, seed=10010, ncores=4)
#
# se.elevated.its2.bstars <- spiec.easi(elevated.its2, method='mb', lambda.min.ratio=1e-1, nlambda=100,
# sel.criterion='bstars', pulsar.select=TRUE, pulsar.params=pargs2)
#
# getStability(se.elevated.its2.bstars) #
#
# save(se.elevated.its2.bstars, file = paste0(net.loc, "/spiec_nets_its2_ele.bstars.RData"))
# se.amb.its2.bstars <- spiec.easi(elevated.its2, method='mb', lambda.min.ratio=1e-1, nlambda=100,
# sel.criterion='bstars', pulsar.select=TRUE, pulsar.params=pargs2)
#
# getStability(se.amb.its2.bstars) #
#
# bac
# gen.se.elevated.bac <- spiec.easi(elevated.16s, method='mb', lambda.min.ratio=1e-2, nlambda=100, pulsar.params=list(rep.num=50))
# changing lambda min ration because stability is kinda low. Alternative could be to raise nlambda but 100 was what the troublehooting guide recommended on the high side
# gen.se.elevated.bac <- spiec.easi(elevated.16s, method='mb', lambda.min.ratio=1e-1, nlambda=100, pulsar.params=list(rep.num=50))
#
# getStability(gen.se.elevated.bac) # 0.0462359 better!
# gen.se.elevated.bac$select$stars$summary
#
# #
# gen.se.amb.bac <- spiec.easi(amb.16s, method='mb', lambda.min.ratio=1e-1, nlambda=100, pulsar.params=list(rep.num=50))
#
# getStability(gen.se.amb.bac) # 0.04755.2 Save networks / work from a saved copy if necessary
#save(se.elevated.bac, se.amb.bac, file = paste0(net.loc, "/spiec_nets_16s.RData"))
#save(se.elevated.its1, se.amb.its1, file = paste0(net.loc, "spiec_nets_ITS1.RData"))
#save(se.amb.its2.bstars, se.elevated.its2.bstars, file = paste0(net.loc, "/spiec_nets_its2.RData"))
if(!"se.elevated.its1" %in% names(globalenv()))
{load(paste0(net.loc,"/spiec_nets_ITS1.RData"))}
if(!"se.elevated.bac" %in% names(globalenv()))
{load(paste0(net.loc,"/spiec_nets_16s.RData"))}
if(!"se.elevated.its2.bstars" %in% names(globalenv()))
{load(paste0(net.loc,"/spiec_nets_its2.RData"))}5.3 Plot networks
ITS1
Elevated
# plot within phyloseq framework
its1.ele.mb <- adj2igraph(getRefit(se.elevated.its1), vertex.attr=list(name=taxa_names(phylo.all$elevated.its1)))
p.its1.el= plot_network(its1.ele.mb, phylo.all$elevated.its1, type='taxa', color="Family.legend", label= NULL, point_size = 0.5, alpha= 0.5, line_alpha = 0.4, title = expression(paste("Elevated ", CO[2])))
# can do further ggplot functions
p.its1.el= p.its1.el +
theme(legend.position = "none")Ambient
its1.amb.mb <- adj2igraph(getRefit(se.amb.its1), vertex.attr=list(name=taxa_names(phylo.all$amb.its1)))
p.its1.amb= plot_network(its1.amb.mb, phylo.all$amb.its1, type='taxa', color="Family.legend", label= NULL, point_size = 0.5, alpha= 0.5, line_alpha = 0.4, title = expression(paste("Ambient ", CO[2])))
p.its1.amb.2= p.its1.amb +
guides(color=guide_legend(ncol=2)) +
theme(legend.position = "none")
test= p.its1.amb +
labs(color = "") +
theme_void(base_size = 10) + guides(color = guide_legend(override.aes = list(size=3)))# Extract the legend. Returns a gtable
leg <- ggpubr::get_legend(test)
# Convert to a ggplot and print
leg.plot=as_ggplot(leg) Make a multiplot
p1= plot_grid(p.its1.amb.2, p.its1.el, labels = c('A', 'B'), hjust = 0.5)
p1.final= plot_grid(p1, NULL, leg.plot, ncol=1, align="v", rel_heights = c(1, 0, 1))
ggsave(paste0(output.loc,"/figureS3.jpg"),p1.final, height= 10)## Saving 7 x 10 in imageggsave(paste0(output.loc,"/figureS3.pdf"),p1.final, height= 10)## Saving 7 x 10 in imageITS2
# plot within phyloseq framework
el.its2.mb <- adj2igraph(getRefit(se.elevated.its2.bstars), vertex.attr=list(name=taxa_names(phylo.all$elevated.its2)))
p.its2.el= plot_network(el.its2.mb, phylo.all$elevated.its2, type='taxa', color="Family.legend", label= NULL, point_size = 0.5, alpha= 0.5, line_alpha = 0.4, title = expression(paste("Elevated ", CO[2])))
# can do further ggplot functions
p.its2.el= p.its2.el +
theme(legend.position = "none")am.its2.mb <- adj2igraph(getRefit(se.amb.its2.bstars), vertex.attr=list(name=taxa_names(phylo.all$amb.its2)))
p.its2.am= plot_network(am.its2.mb, phylo.all$amb.its2, type='taxa', color="Family.legend", label= NULL, point_size = 0.5, alpha= 0.5, line_alpha = 0.4, title = expression(paste("Ambient ", CO[2])))
# can do further ggplot functions
p.its2.amb.2= p.its2.am +
guides(color=guide_legend(ncol=2)) +
theme(legend.position = "none")
#for the legend
leg.its2= p.its2.am +
labs(color = "") +
theme_void(base_size = 10) + guides(color = guide_legend(override.aes = list(size=3)))# Extract the legend. Returns a gtable
leg.its2 <- ggpubr::get_legend(leg.its2)
# Convert to a ggplot and print
leg.its2.plot=ggpubr::as_ggplot(leg.its2) Make a multiplot
p1.its2= plot_grid(p.its2.amb.2, p.its2.el, labels = c('A', 'B'), hjust = 0.5)
p1.its2.final= plot_grid(p1.its2, NULL, leg.its2.plot, ncol=1, align="v", rel_heights = c(1, 0, 1))
ggsave(paste0(output.loc,"/figure2.jpg"),p1.its2.final, height= 10)## Saving 7 x 10 in imageggsave(paste0(output.loc,"/figure2.pdf"),p1.its2.final, height= 10)## Saving 7 x 10 in image16s
#bac
bac.el.mb <- adj2igraph(getRefit(se.elevated.bac), vertex.attr=list(name=taxa_names(phylo.all$elevated.16s)))
p.16s.el= plot_network(bac.el.mb, phylo.all$elevated.16s, type='taxa', color="Genus", point_size = 1, alpha= 0.5, line_alpha = 0.4, label= NULL, title = expression(paste("Elevated ", CO[2])))
p.16s.el= p.16s.el + theme(legend.position = "none")bac.amb.mb <- adj2igraph(getRefit(se.amb.bac), vertex.attr=list(name=taxa_names(phylo.all$amb.16s)))
p.16s.amb= plot_network(bac.amb.mb, phylo.all$amb.16s, type='taxa', color="Genus", point_size = 1, alpha= 0.5, line_alpha = 0.4, label= NULL, title = expression(paste("Ambient ", CO[2])))
p.16s.amb= p.16s.amb + theme(legend.position = "none")
#make legend edits and save to additional plot
bac.leg= p.16s.amb +
labs(color = "") +
theme_void(base_size = 10) + guides(color = guide_legend(override.aes = list(size=3)))# Extract the legend. Returns a gtable
bac.leg.extract <- ggpubr::get_legend(bac.leg)
# Convert to a ggplot and print
bac.leg.plot=as_ggplot(bac.leg.extract) Make a multiplot
bac1= plot_grid(p.16s.amb, p.16s.el, labels = c('A', 'B'), hjust = 0.5)
bac1.final= plot_grid(bac1, NULL, bac.leg.plot, ncol=1, align="v", rel_heights = c(1, 0, 1))
ggsave(paste0(output.loc,"/figure3.jpg"), bac1.final, height= 10)## Saving 7 x 10 in image5.4 Compare networks
Start with nets already made from spieceasi
# Make association matrix
# its1
assoMat.its1.el <- as.matrix(SpiecEasi::symBeta(getOptBeta(se.elevated.its1)))
assoMat.its1.am <- as.matrix(SpiecEasi::symBeta(getOptBeta(se.amb.its1)))
rownames(assoMat.its1.el) <- colnames(assoMat.its1.el) <- colnames(se.elevated.its1$est$data)
rownames(assoMat.its1.am) <- colnames(assoMat.its1.am) <- colnames(se.amb.its1$est$data)
net_its1_comp <- net_asso <- netConstruct(data = assoMat.its1.el, data2= assoMat.its1.am,
dataType = "condDependence",
sparsMethod = "none",
verbose = 0)
# its2
assoMat.its2.el <- as.matrix(SpiecEasi::symBeta(getOptBeta(se.elevated.its2.bstars)))
assoMat.its2.am <- as.matrix(SpiecEasi::symBeta(getOptBeta(se.amb.its2.bstars)))
rownames(assoMat.its2.el) <- colnames(assoMat.its2.el) <- colnames(se.elevated.its2.bstars$est$data)
rownames(assoMat.its2.am) <- colnames(assoMat.its2.am) <- colnames(se.amb.its2.bstars$est$data)
net_its2_comp <- net_asso <- netConstruct(data = assoMat.its2.el, data2= assoMat.its2.am,
dataType = "condDependence",
sparsMethod = "none",
verbose = 0)
# 16s
assoMat.bac.el <- as.matrix(SpiecEasi::symBeta(getOptBeta(se.elevated.bac)))
assoMat.bac.am <- as.matrix(SpiecEasi::symBeta(getOptBeta(se.amb.bac)))
rownames(assoMat.bac.el) <- colnames(assoMat.bac.el) <- colnames(se.elevated.bac$est$data)
rownames(assoMat.bac.am) <- colnames(assoMat.bac.am) <- colnames(se.amb.bac$est$data)
net_16s_comp <- net_asso <- netConstruct(data = assoMat.bac.el, data2= assoMat.bac.am,
dataType = "condDependence",
sparsMethod = "none",
verbose = 0)5.5 Analyze network properties
Determine network properties for objects of class microNet
# Using eigenvector centrality as hub score
#its1
comp_its1_props1 <- netAnalyze(net_its1_comp, clustMethod = "cluster_fast_greedy", hubPar = "eigenvector")
plot(comp_its1_props1, groupNames = c("Elevated", "Ambient"))
outputits1.comp.props= summary(comp_its1_props1, groupNames = c("Elevated", "Ambient"))
#its2
comp_its2_props1 <- netAnalyze(net_its2_comp, clustMethod = "cluster_fast_greedy", hubPar = "eigenvector")
plot(comp_its2_props1, groupNames = c("Elevated", "Ambient"))
outputits2.comp.props= summary(comp_its2_props1, groupNames = c("Elevated", "Ambient"))
#16s
comp_16s_props1 <- netAnalyze(net_16s_comp, clustMethod = "cluster_fast_greedy", hubPar = "eigenvector")
plot(comp_16s_props1, groupNames = c("Elevated", "Ambient"))
output16s.comp.props= summary(comp_16s_props1, groupNames = c("Elevated", "Ambient"))5.6 Quantitative network comparison
#its1
comp_its1 <- netCompare(comp_its1_props1,
permTest = FALSE,
verbose = FALSE,
seed = 123456)
sum.comp.its1=summary(comp_its1,
groupNames = c("Elevated CO2", "Ambient CO2"),
showCentr = c("degree", "between", "closeness"),
numbNodes = 5)
#its2
comp_its2 <- netCompare(comp_its2_props1,
permTest = FALSE,
verbose = FALSE,
seed = 123456)
sum.comp.its2=summary(comp_its2,
groupNames = c("Elevated CO2", "Ambient CO2"),
showCentr = c("degree", "between", "closeness"),
numbNodes = 5)
#16s
comp_bac <- netCompare(comp_16s_props1,
permTest = FALSE,
verbose = FALSE,
seed = 123456)
sum.comp.bac=summary(comp_bac,
groupNames = c("Elevated CO2", "Ambient CO2"),
showCentr = c("degree", "between", "closeness"),
numbNodes = 5)5.7 Make / output tables of relevant metrics
#hubs
hubs.bac= output16s.comp.props$hubs
hubs.bac$dataset <- "16s"
hubs.its1=outputits1.comp.props$hubs
hubs.its1$dataset <- "ITS1"
hubs.its2=outputits2.comp.props$hubs
hubs.its2$dataset <- "ITS2"
hubs= rbind(hubs.bac, hubs.its1)
hubs= rbind(hubs, hubs.its2)
write.csv(hubs, paste0(output.loc, "/hub.taxa.all.csv"))
# netcomp
netmets= sum.comp.its1$propdiffs[1:5,]
netmets$dataset <- "ITS1"
netmets=netmets %>% rownames_to_column("metric")
netmets.its2= sum.comp.its2$propdiffs[1:5,]
netmets.its2$dataset <- "ITS2"
netmets.its2=netmets.its2 %>% rownames_to_column("metric")
netmets.bac=sum.comp.bac$propdiffs[1:5,]
netmets.bac$dataset <- "16s"
netmets.bac= netmets.bac %>% rownames_to_column("metric")
netmets= rbind(netmets, netmets.bac)
netmets= rbind(netmets, netmets.its2)
colnames(netmets) <- c("metric", "Elevated CO2" , "Ambient CO2" ,"difference", "dataset")
write.csv(netmets, paste0(output.loc, "/net.metrics.all.csv"))6 SUPPLEMENTAL
Compare ITS primers at the Genus and Family levels
its1.gen.unique= unique(its1.tax$Genus)
its2.gen.unique= unique(its2.tax$Genus)
its1.fam.unique= unique(its1.tax$Family)
its2.fam.unique= unique(its2.tax$Family)
#remove NA
its1.gen.unique= its1.gen.unique[!is.na(its1.gen.unique)]
its2.gen.unique= its2.gen.unique[!is.na(its2.gen.unique)]
its1.fam.unique= its1.fam.unique[!is.na(its1.fam.unique)]
its2.fam.unique= its2.fam.unique[!is.na(its2.fam.unique)]
# look at what is not shared
setdiff(its1.gen.unique, its2.gen.unique) #32 genera found in its1 not in its2## [1] "g__Pseudopithomyces" "g__Paraboeremia" "g__Mycosphaerella"
## [4] "g__Malassezia" "g__Lectera" "g__Neohelicomyces"
## [7] "g__Naganishia" "g__Clitopilus" "g__Schizophyllum"
## [10] "g__Setoseptoria" "g__Pyrenochaetopsis" "g__Fomitopsis"
## [13] "g__Sistotrema" "g__Rhodotorula" "g__Steccherinum"
## [16] "g__Bullera" "g__Exidia" "g__Ceriporia"
## [19] "g__Coprinellus" "g__Roussoella" "g__Paracylindrocarpon"
## [22] "g__Neocosmospora" "g__Symmetrospora" "g__Phaeopoacea"
## [25] "g__Aspergillus" "g__Vagicola" "g__Neodevriesia"
## [28] "g__Tomentella" "g__Psilocybe" "g__Pseudoophiobolus"
## [31] "g__Bulleribasidium" "g__Phomatospora"setdiff(its2.gen.unique, its1.gen.unique) #33 general found in its2 not in its1## [1] "g__Cercospora" "g__Didymocyrtis" "g__Murispora"
## [4] "g__Blakeslea" "g__Preussia" "g__Gibellulopsis"
## [7] "g__Talaromyces" "g__Xylodon" "g__Subplenodomus"
## [10] "g__Hymenoscyphus" "g__Pestalotiopsis" "g__Phyllozyma"
## [13] "g__Hyphoderma" "g__Poitrasia" "g__Paraphoma"
## [16] "g__Plenodomus" "g__Ceratobasidium" "g__Oliveonia"
## [19] "g__Waitea" "g__Sampaiozyma" "g__Neptunomyces"
## [22] "g__Trechispora" "g__Hyphodermella" "g__Flavodon"
## [25] "g__Penicillium" "g__Helicodendron" "g__Laetisaria"
## [28] "g__Sclerotrema" "g__Moesziomyces" "g__Neoroussoella"
## [31] "g__Mycena" "g__Kurtzmanomyces" "g__Ciliophora"setdiff(its1.fam.unique, its2.fam.unique) #15 families found in its1 not in its2## [1] "f__Malasseziaceae"
## [2] "f__Tubeufiaceae"
## [3] "f__Entolomataceae"
## [4] "f__Schizophyllaceae"
## [5] "f__Cucurbitariaceae"
## [6] "f__Fomitopsidaceae"
## [7] "f__Lycoperdaceae"
## [8] "f__Cantharellales_fam_Incertae_sedis"
## [9] "f__Steccherinaceae"
## [10] "f__Bulleraceae"
## [11] "f__Exidiaceae"
## [12] "f__Symmetrosporaceae"
## [13] "f__Thelephoraceae"
## [14] "f__Tilletiaceae"
## [15] "f__Phomatosporaceae"setdiff(its2.fam.unique, its1.fam.unique) #20 families found in its2 not in its1## [1] "f__Amniculicolaceae"
## [2] "f__Choanephoraceae"
## [3] "f__Sporormiaceae"
## [4] "f__Trichocomaceae"
## [5] "f__Tetraplosphaeriaceae"
## [6] "f__Schizoporaceae"
## [7] "f__Sporocadaceae"
## [8] "f__Spiculogloeaceae"
## [9] "f__Hyphodermataceae"
## [10] "f__Auriculariales_fam_Incertae_sedis"
## [11] "f__Trichomeriaceae"
## [12] "f__Xylariaceae"
## [13] "f__Chrysozymaceae"
## [14] "f__Hydnodontaceae"
## [15] "f__Phanerochaetaceae"
## [16] "f__Lophiostomataceae"
## [17] "f__Ustilaginaceae"
## [18] "f__Cordycipitaceae"
## [19] "f__Chionosphaeraceae"
## [20] "f__Pezizomycotina_fam_Incertae_sedis"# overlap
overlap.genus=intersect(its1.gen.unique,its2.gen.unique)
overlap.fam=intersect(its1.fam.unique,its2.fam.unique)
#proportion of taxa overlap
length(overlap.genus)/(length(overlap.genus) + length(setdiff(its1.gen.unique, its2.gen.unique))+ length(
setdiff(its2.gen.unique, its1.gen.unique))) # 47.81% taxa are shared at the genus level## [1] 0.4758065length(overlap.fam)/(length(overlap.fam) + length(setdiff(its1.fam.unique, its2.fam.unique))+ length(
setdiff(its2.fam.unique, its1.fam.unique))) # 55.70% taxa are shared at the fam level## [1] 0.5512821Venn diagrams
fam.list=list(ITS1= its1.fam.unique, ITS2= its2.fam.unique)
genera.list=list(ITS1= its1.gen.unique, ITS2= its2.gen.unique)
fam.venn=ggVennDiagram(fam.list) +
scale_fill_gradient(low="grey90",high = "red") +
labs(title = "Taxa overlap by family")
genera.venn=ggVennDiagram(genera.list,) + scale_fill_gradient(low="grey90",high = "red") +
labs(title = "Taxa overlap by genera")
ggsave(paste0(output.loc,"/figureS1.fam.fenn.pdf"), fam.venn)## Saving 8 x 5 in imageggsave(paste0(output.loc,"/figureS2.genera.fenn.pdf"), genera.venn)## Saving 8 x 5 in image